Starting phenix.real_space_refine on Sat Dec 28 11:23:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wq4_32699/12_2024/7wq4_32699.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wq4_32699/12_2024/7wq4_32699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wq4_32699/12_2024/7wq4_32699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wq4_32699/12_2024/7wq4_32699.map" model { file = "/net/cci-nas-00/data/ceres_data/7wq4_32699/12_2024/7wq4_32699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wq4_32699/12_2024/7wq4_32699.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5277 2.51 5 N 1451 2.21 5 O 1509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8290 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2225 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 12, 'TRANS': 269} Chain breaks: 1 Chain: "L" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 95 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Chain: "A" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1927 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "G" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 414 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.23, per 1000 atoms: 0.63 Number of scatterers: 8290 At special positions: 0 Unit cell: (88.218, 97.344, 123.708, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1509 8.00 N 1451 7.00 C 5277 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 175 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 991.6 milliseconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 42.5% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'R' and resid 26 through 52 removed outlier: 3.907A pdb=" N LEU R 30 " --> pdb=" O VAL R 26 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL R 49 " --> pdb=" O LEU R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 88 Proline residue: R 80 - end of helix Processing helix chain 'R' and resid 95 through 100 removed outlier: 4.096A pdb=" N LYS R 99 " --> pdb=" O SER R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 129 removed outlier: 3.720A pdb=" N PHE R 106 " --> pdb=" O HIS R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 158 Processing helix chain 'R' and resid 159 through 164 removed outlier: 4.166A pdb=" N TYR R 164 " --> pdb=" O TYR R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 196 Processing helix chain 'R' and resid 196 through 215 Processing helix chain 'R' and resid 224 through 249 removed outlier: 3.794A pdb=" N ARG R 228 " --> pdb=" O GLY R 224 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TRP R 249 " --> pdb=" O PHE R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 262 removed outlier: 3.515A pdb=" N HIS R 253 " --> pdb=" O TRP R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 293 removed outlier: 3.696A pdb=" N ASN R 284 " --> pdb=" O VAL R 280 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) Proline residue: R 289 - end of helix Processing helix chain 'R' and resid 296 through 301 removed outlier: 3.642A pdb=" N ARG R 300 " --> pdb=" O SER R 296 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS R 301 " --> pdb=" O LYS R 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 296 through 301' Processing helix chain 'R' and resid 302 through 307 removed outlier: 3.528A pdb=" N ILE R 306 " --> pdb=" O GLY R 302 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS R 307 " --> pdb=" O PHE R 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 302 through 307' Processing helix chain 'L' and resid 3 through 12 removed outlier: 3.554A pdb=" N GLY L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.583A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 114 through 130 removed outlier: 4.077A pdb=" N GLN A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLU A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.588A pdb=" N LEU A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 164 through 170 Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.549A pdb=" N PHE A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 removed outlier: 3.840A pdb=" N PHE A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.602A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.641A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.022A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.845A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.518A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'R' and resid 165 through 169 Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 76 removed outlier: 4.181A pdb=" N VAL A 86 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY A 40 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.508A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.688A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.541A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.683A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 192 removed outlier: 4.110A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 7.068A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.608A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.316A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2702 1.34 - 1.46: 1972 1.46 - 1.58: 3709 1.58 - 1.70: 10 1.70 - 1.81: 74 Bond restraints: 8467 Sorted by residual: bond pdb=" C5 CLR R 402 " pdb=" C6 CLR R 402 " ideal model delta sigma weight residual 1.332 1.651 -0.319 2.00e-02 2.50e+03 2.54e+02 bond pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " ideal model delta sigma weight residual 1.332 1.650 -0.318 2.00e-02 2.50e+03 2.53e+02 bond pdb=" C15 CLR R 402 " pdb=" C16 CLR R 402 " ideal model delta sigma weight residual 1.541 1.708 -0.167 2.00e-02 2.50e+03 6.99e+01 bond pdb=" C15 CLR R 401 " pdb=" C16 CLR R 401 " ideal model delta sigma weight residual 1.541 1.705 -0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" C8 CLR R 402 " pdb=" C9 CLR R 402 " ideal model delta sigma weight residual 1.535 1.671 -0.136 2.00e-02 2.50e+03 4.62e+01 ... (remaining 8462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 11412 2.71 - 5.41: 58 5.41 - 8.12: 12 8.12 - 10.83: 3 10.83 - 13.53: 4 Bond angle restraints: 11489 Sorted by residual: angle pdb=" N VAL R 295 " pdb=" CA VAL R 295 " pdb=" C VAL R 295 " ideal model delta sigma weight residual 113.71 106.66 7.05 9.50e-01 1.11e+00 5.51e+01 angle pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " pdb=" C7 CLR R 401 " ideal model delta sigma weight residual 125.11 111.58 13.53 3.00e+00 1.11e-01 2.04e+01 angle pdb=" C5 CLR R 402 " pdb=" C6 CLR R 402 " pdb=" C7 CLR R 402 " ideal model delta sigma weight residual 125.11 111.81 13.30 3.00e+00 1.11e-01 1.97e+01 angle pdb=" CA ALA R 170 " pdb=" C ALA R 170 " pdb=" O ALA R 170 " ideal model delta sigma weight residual 122.03 117.50 4.53 1.17e+00 7.31e-01 1.50e+01 angle pdb=" C10 CLR R 401 " pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " ideal model delta sigma weight residual 122.94 111.81 11.13 3.00e+00 1.11e-01 1.38e+01 ... (remaining 11484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.16: 4849 12.16 - 24.32: 191 24.32 - 36.47: 60 36.47 - 48.63: 26 48.63 - 60.79: 9 Dihedral angle restraints: 5135 sinusoidal: 2094 harmonic: 3041 Sorted by residual: dihedral pdb=" N PHE B 234 " pdb=" CA PHE B 234 " pdb=" CB PHE B 234 " pdb=" CG PHE B 234 " ideal model delta sinusoidal sigma weight residual -180.00 -120.16 -59.84 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG R 184 " pdb=" CA ARG R 184 " pdb=" CB ARG R 184 " pdb=" CG ARG R 184 " ideal model delta sinusoidal sigma weight residual -60.00 -117.77 57.77 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CG ARG R 184 " pdb=" CD ARG R 184 " pdb=" NE ARG R 184 " pdb=" CZ ARG R 184 " ideal model delta sinusoidal sigma weight residual 180.00 139.10 40.90 2 1.50e+01 4.44e-03 9.14e+00 ... (remaining 5132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1271 0.110 - 0.221: 27 0.221 - 0.331: 4 0.331 - 0.442: 2 0.442 - 0.552: 2 Chirality restraints: 1306 Sorted by residual: chirality pdb=" C13 CLR R 402 " pdb=" C12 CLR R 402 " pdb=" C14 CLR R 402 " pdb=" C17 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.93 -2.38 -0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" C13 CLR R 401 " pdb=" C12 CLR R 401 " pdb=" C14 CLR R 401 " pdb=" C17 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.93 -2.39 -0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" C9 CLR R 402 " pdb=" C10 CLR R 402 " pdb=" C11 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.45 -2.86 0.42 2.00e-01 2.50e+01 4.35e+00 ... (remaining 1303 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 101 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" C VAL R 101 " 0.021 2.00e-02 2.50e+03 pdb=" O VAL R 101 " -0.008 2.00e-02 2.50e+03 pdb=" N HIS R 102 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO B 236 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 158 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.12e+00 pdb=" N PRO R 159 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 159 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 159 " -0.015 5.00e-02 4.00e+02 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 2 2.10 - 2.80: 2089 2.80 - 3.50: 11004 3.50 - 4.20: 19240 4.20 - 4.90: 34386 Nonbonded interactions: 66721 Sorted by model distance: nonbonded pdb=" OD1 ASN N 35 " pdb=" CB ASP N 50 " model vdw 1.399 3.440 nonbonded pdb=" CG2 VAL R 174 " pdb=" NE2 HIS R 176 " model vdw 2.067 3.540 nonbonded pdb=" O TYR R 129 " pdb=" OG SER R 133 " model vdw 2.247 3.040 nonbonded pdb=" O THR R 191 " pdb=" OG SER R 195 " model vdw 2.250 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.289 3.040 ... (remaining 66716 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.770 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:17.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.319 8467 Z= 0.442 Angle : 0.615 13.533 11489 Z= 0.339 Chirality : 0.052 0.552 1306 Planarity : 0.003 0.027 1450 Dihedral : 8.519 60.788 3162 Min Nonbonded Distance : 1.399 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.45 % Allowed : 3.38 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.24), residues: 1032 helix: 0.15 (0.26), residues: 373 sheet: -0.58 (0.31), residues: 237 loop : -1.48 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.000 HIS A 209 PHE 0.010 0.001 PHE R 103 TYR 0.005 0.001 TYR N 60 ARG 0.001 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 251 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: R 184 ARG cc_start: 0.5524 (OUTLIER) cc_final: 0.4897 (mtp-110) REVERT: A 15 ARG cc_start: 0.6050 (ttt90) cc_final: 0.5842 (ttm-80) REVERT: A 17 LYS cc_start: 0.6310 (mttt) cc_final: 0.5857 (pttp) REVERT: A 69 ILE cc_start: 0.8297 (mt) cc_final: 0.8074 (mm) REVERT: A 75 GLN cc_start: 0.7309 (tt0) cc_final: 0.6941 (tm130) REVERT: A 191 TYR cc_start: 0.7616 (m-10) cc_final: 0.7346 (m-10) REVERT: A 208 ARG cc_start: 0.6356 (mtm-85) cc_final: 0.5995 (tpt90) REVERT: B 44 GLN cc_start: 0.7850 (mt0) cc_final: 0.7582 (mt0) REVERT: B 188 MET cc_start: 0.8239 (mmm) cc_final: 0.8029 (mmm) REVERT: B 197 ARG cc_start: 0.6792 (mtm180) cc_final: 0.6497 (mtp85) REVERT: B 234 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: B 254 ASP cc_start: 0.7784 (p0) cc_final: 0.7549 (p0) REVERT: N 65 LYS cc_start: 0.7321 (mttt) cc_final: 0.6892 (tmtt) REVERT: N 80 TYR cc_start: 0.6848 (m-80) cc_final: 0.6631 (m-80) outliers start: 4 outliers final: 0 residues processed: 255 average time/residue: 1.2715 time to fit residues: 343.0321 Evaluate side-chains 167 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 184 ARG Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.0370 chunk 77 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 55 GLN R 82 GLN R 253 HIS A 52 GLN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 GLN B 35 ASN B 91 HIS B 176 GLN B 220 GLN B 259 GLN N 77 ASN G 11 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8467 Z= 0.196 Angle : 0.520 7.319 11489 Z= 0.272 Chirality : 0.042 0.142 1306 Planarity : 0.004 0.028 1450 Dihedral : 5.145 55.945 1286 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.27 % Allowed : 13.85 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.26), residues: 1032 helix: 1.56 (0.26), residues: 384 sheet: -0.18 (0.32), residues: 231 loop : -0.78 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 332 HIS 0.015 0.002 HIS R 176 PHE 0.023 0.002 PHE A 108 TYR 0.013 0.001 TYR A 243 ARG 0.006 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: R 88 LEU cc_start: 0.6207 (mt) cc_final: 0.5862 (mt) REVERT: R 96 LEU cc_start: 0.5828 (pt) cc_final: 0.5221 (tp) REVERT: R 166 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7092 (tt0) REVERT: A 8 GLU cc_start: 0.6248 (mm-30) cc_final: 0.6028 (mm-30) REVERT: A 15 ARG cc_start: 0.6265 (ttt90) cc_final: 0.6043 (ttm-80) REVERT: A 73 LYS cc_start: 0.8579 (mttp) cc_final: 0.8205 (mttt) REVERT: A 78 LYS cc_start: 0.8353 (mmtp) cc_final: 0.7496 (mmtt) REVERT: A 208 ARG cc_start: 0.6665 (mtm-85) cc_final: 0.6093 (tpt90) REVERT: A 222 GLU cc_start: 0.7187 (pm20) cc_final: 0.6673 (pt0) REVERT: A 230 ASP cc_start: 0.7447 (m-30) cc_final: 0.7162 (m-30) REVERT: B 44 GLN cc_start: 0.8017 (mt0) cc_final: 0.7770 (mt0) REVERT: B 57 LYS cc_start: 0.8589 (pttm) cc_final: 0.8215 (pttt) REVERT: B 186 ASP cc_start: 0.7880 (m-30) cc_final: 0.7368 (m-30) REVERT: B 188 MET cc_start: 0.8324 (mmm) cc_final: 0.7777 (mmm) REVERT: B 197 ARG cc_start: 0.6973 (mtm180) cc_final: 0.6593 (mtp85) REVERT: B 212 ASP cc_start: 0.7168 (t0) cc_final: 0.6880 (t70) REVERT: B 214 ARG cc_start: 0.7285 (mmt180) cc_final: 0.6850 (mmt180) REVERT: B 234 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.7727 (m-80) REVERT: B 254 ASP cc_start: 0.7764 (p0) cc_final: 0.7495 (p0) REVERT: B 263 THR cc_start: 0.7916 (t) cc_final: 0.7586 (m) REVERT: B 325 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7977 (mmt) outliers start: 29 outliers final: 11 residues processed: 188 average time/residue: 1.2899 time to fit residues: 257.1218 Evaluate side-chains 156 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.5980 chunk 28 optimal weight: 0.0970 chunk 77 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8467 Z= 0.239 Angle : 0.551 6.350 11489 Z= 0.291 Chirality : 0.043 0.138 1306 Planarity : 0.004 0.029 1450 Dihedral : 5.020 56.589 1282 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.62 % Allowed : 15.20 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1032 helix: 1.46 (0.27), residues: 397 sheet: 0.14 (0.32), residues: 228 loop : -0.72 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 332 HIS 0.011 0.001 HIS A 209 PHE 0.015 0.002 PHE B 151 TYR 0.010 0.002 TYR R 86 ARG 0.006 0.001 ARG R 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: R 35 ILE cc_start: 0.6769 (OUTLIER) cc_final: 0.6540 (mt) REVERT: R 96 LEU cc_start: 0.5808 (pt) cc_final: 0.5230 (tp) REVERT: R 122 ASP cc_start: 0.8078 (t70) cc_final: 0.7800 (t70) REVERT: R 136 LEU cc_start: 0.7516 (tt) cc_final: 0.7206 (tp) REVERT: R 166 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.6919 (tt0) REVERT: R 298 HIS cc_start: 0.6664 (t70) cc_final: 0.6183 (m-70) REVERT: A 15 ARG cc_start: 0.6286 (ttt90) cc_final: 0.5928 (ttm-80) REVERT: A 20 GLU cc_start: 0.6556 (tp30) cc_final: 0.6144 (tp30) REVERT: A 73 LYS cc_start: 0.8579 (mttp) cc_final: 0.8013 (mttt) REVERT: A 75 GLN cc_start: 0.8108 (tt0) cc_final: 0.7906 (tt0) REVERT: A 78 LYS cc_start: 0.8534 (mmtp) cc_final: 0.7602 (mptt) REVERT: A 82 HIS cc_start: 0.7652 (m170) cc_final: 0.7279 (m170) REVERT: A 208 ARG cc_start: 0.6855 (mtm-85) cc_final: 0.6272 (mmm-85) REVERT: A 222 GLU cc_start: 0.7137 (pm20) cc_final: 0.6754 (pt0) REVERT: B 29 THR cc_start: 0.6611 (OUTLIER) cc_final: 0.5828 (p) REVERT: B 57 LYS cc_start: 0.8530 (pttm) cc_final: 0.8132 (pttt) REVERT: B 186 ASP cc_start: 0.7994 (m-30) cc_final: 0.7573 (m-30) REVERT: B 188 MET cc_start: 0.8054 (mmm) cc_final: 0.7494 (mmm) REVERT: B 197 ARG cc_start: 0.7025 (mtm180) cc_final: 0.6611 (mtp85) REVERT: B 212 ASP cc_start: 0.7603 (t0) cc_final: 0.7227 (t0) REVERT: B 214 ARG cc_start: 0.7537 (mmt180) cc_final: 0.7217 (mpp-170) REVERT: B 220 GLN cc_start: 0.7622 (tt0) cc_final: 0.7332 (tt0) REVERT: B 234 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.7565 (m-80) REVERT: B 263 THR cc_start: 0.8294 (t) cc_final: 0.7824 (m) REVERT: B 329 THR cc_start: 0.8714 (m) cc_final: 0.8452 (t) REVERT: G 37 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7249 (mp) REVERT: G 42 GLU cc_start: 0.7138 (pp20) cc_final: 0.6501 (mm-30) outliers start: 41 outliers final: 19 residues processed: 173 average time/residue: 1.3611 time to fit residues: 249.3015 Evaluate side-chains 148 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 55 optimal weight: 0.3980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8467 Z= 0.285 Angle : 0.572 6.777 11489 Z= 0.301 Chirality : 0.044 0.159 1306 Planarity : 0.004 0.033 1450 Dihedral : 5.193 58.321 1282 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.73 % Allowed : 17.57 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.26), residues: 1032 helix: 1.61 (0.27), residues: 391 sheet: 0.43 (0.32), residues: 225 loop : -0.66 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.011 0.001 HIS A 209 PHE 0.015 0.002 PHE B 151 TYR 0.013 0.002 TYR R 86 ARG 0.006 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: R 122 ASP cc_start: 0.7996 (t70) cc_final: 0.7603 (t70) REVERT: R 136 LEU cc_start: 0.7489 (tt) cc_final: 0.7186 (tp) REVERT: R 166 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.6941 (tt0) REVERT: R 196 TYR cc_start: 0.8312 (t80) cc_final: 0.8097 (t80) REVERT: R 298 HIS cc_start: 0.7112 (t70) cc_final: 0.6229 (m-70) REVERT: A 15 ARG cc_start: 0.6355 (ttt90) cc_final: 0.5836 (ttm-80) REVERT: A 20 GLU cc_start: 0.6684 (tp30) cc_final: 0.6276 (tp30) REVERT: A 73 LYS cc_start: 0.8638 (mttp) cc_final: 0.8227 (mttt) REVERT: A 78 LYS cc_start: 0.8529 (mmtp) cc_final: 0.7613 (mptt) REVERT: A 194 ARG cc_start: 0.7388 (ttp80) cc_final: 0.7158 (ttt-90) REVERT: A 208 ARG cc_start: 0.7027 (mtm-85) cc_final: 0.6291 (mmm-85) REVERT: B 57 LYS cc_start: 0.8475 (pttm) cc_final: 0.8021 (pttt) REVERT: B 134 ARG cc_start: 0.6750 (ptm-80) cc_final: 0.6042 (tpp-160) REVERT: B 186 ASP cc_start: 0.8125 (m-30) cc_final: 0.7767 (m-30) REVERT: B 188 MET cc_start: 0.8062 (mmm) cc_final: 0.7552 (mmm) REVERT: B 197 ARG cc_start: 0.7238 (mtm180) cc_final: 0.6808 (mtp85) REVERT: B 212 ASP cc_start: 0.7846 (t0) cc_final: 0.7603 (t0) REVERT: B 214 ARG cc_start: 0.7631 (mmt180) cc_final: 0.7321 (mpp-170) REVERT: B 220 GLN cc_start: 0.7692 (tt0) cc_final: 0.7328 (tt0) REVERT: B 263 THR cc_start: 0.8332 (t) cc_final: 0.7829 (m) REVERT: G 37 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7236 (mp) REVERT: G 42 GLU cc_start: 0.7091 (pp20) cc_final: 0.6560 (mm-30) outliers start: 42 outliers final: 21 residues processed: 161 average time/residue: 1.3352 time to fit residues: 227.5538 Evaluate side-chains 150 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN R 82 GLN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN A 75 GLN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8467 Z= 0.233 Angle : 0.536 5.536 11489 Z= 0.284 Chirality : 0.043 0.141 1306 Planarity : 0.004 0.031 1450 Dihedral : 4.901 59.028 1280 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.50 % Allowed : 17.91 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.26), residues: 1032 helix: 1.82 (0.26), residues: 391 sheet: 0.55 (0.33), residues: 224 loop : -0.68 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.008 0.001 HIS A 209 PHE 0.013 0.002 PHE B 151 TYR 0.013 0.001 TYR R 129 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.956 Fit side-chains REVERT: R 122 ASP cc_start: 0.7954 (t70) cc_final: 0.7557 (t70) REVERT: R 136 LEU cc_start: 0.7473 (tt) cc_final: 0.7189 (tp) REVERT: R 166 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.6861 (tt0) REVERT: R 200 VAL cc_start: 0.7274 (OUTLIER) cc_final: 0.7013 (p) REVERT: R 298 HIS cc_start: 0.7135 (t70) cc_final: 0.6211 (m-70) REVERT: A 15 ARG cc_start: 0.6354 (ttt90) cc_final: 0.5807 (ttm-80) REVERT: A 20 GLU cc_start: 0.6673 (tp30) cc_final: 0.6274 (tp30) REVERT: A 28 GLN cc_start: 0.7370 (mm-40) cc_final: 0.7169 (mm-40) REVERT: A 71 GLU cc_start: 0.7743 (tt0) cc_final: 0.7322 (tm-30) REVERT: A 73 LYS cc_start: 0.8678 (mttp) cc_final: 0.8172 (mttp) REVERT: A 78 LYS cc_start: 0.8504 (mmtp) cc_final: 0.7674 (mptt) REVERT: A 208 ARG cc_start: 0.7018 (mtm-85) cc_final: 0.6271 (mmm-85) REVERT: A 222 GLU cc_start: 0.7281 (pm20) cc_final: 0.6765 (pt0) REVERT: A 242 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6585 (tt0) REVERT: B 57 LYS cc_start: 0.8443 (pttm) cc_final: 0.8035 (pttt) REVERT: B 59 TYR cc_start: 0.8150 (OUTLIER) cc_final: 0.7505 (t80) REVERT: B 134 ARG cc_start: 0.6744 (ptm-80) cc_final: 0.6084 (tpp-160) REVERT: B 186 ASP cc_start: 0.8105 (m-30) cc_final: 0.7819 (m-30) REVERT: B 188 MET cc_start: 0.8046 (mmm) cc_final: 0.7605 (mmm) REVERT: B 197 ARG cc_start: 0.7194 (mtm180) cc_final: 0.6801 (mtp85) REVERT: B 212 ASP cc_start: 0.7860 (t0) cc_final: 0.7626 (t0) REVERT: B 214 ARG cc_start: 0.7641 (mmt180) cc_final: 0.7394 (mpp-170) REVERT: B 220 GLN cc_start: 0.7657 (tt0) cc_final: 0.7293 (tt0) REVERT: B 234 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.7560 (m-80) REVERT: B 258 ASP cc_start: 0.6841 (t0) cc_final: 0.6399 (t70) REVERT: B 263 THR cc_start: 0.8375 (t) cc_final: 0.7863 (m) REVERT: B 329 THR cc_start: 0.8693 (m) cc_final: 0.8430 (t) REVERT: G 37 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7217 (mp) REVERT: G 42 GLU cc_start: 0.7047 (pp20) cc_final: 0.6578 (mm-30) outliers start: 40 outliers final: 19 residues processed: 170 average time/residue: 1.3425 time to fit residues: 241.1458 Evaluate side-chains 160 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 11 optimal weight: 0.0040 chunk 56 optimal weight: 4.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8467 Z= 0.149 Angle : 0.481 5.882 11489 Z= 0.254 Chirality : 0.041 0.151 1306 Planarity : 0.003 0.028 1450 Dihedral : 4.527 57.180 1280 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.15 % Allowed : 19.14 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1032 helix: 2.15 (0.27), residues: 391 sheet: 0.56 (0.33), residues: 223 loop : -0.60 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS A 209 PHE 0.011 0.001 PHE B 199 TYR 0.013 0.001 TYR R 129 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 1.499 Fit side-chains revert: symmetry clash REVERT: R 122 ASP cc_start: 0.7916 (t70) cc_final: 0.7561 (t70) REVERT: R 136 LEU cc_start: 0.7382 (tt) cc_final: 0.7101 (tp) REVERT: R 166 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6764 (tt0) REVERT: R 298 HIS cc_start: 0.7069 (t70) cc_final: 0.6050 (m-70) REVERT: A 15 ARG cc_start: 0.6305 (ttt90) cc_final: 0.5812 (ttm-80) REVERT: A 20 GLU cc_start: 0.6510 (tp30) cc_final: 0.6116 (tp30) REVERT: A 28 GLN cc_start: 0.7334 (mm-40) cc_final: 0.7121 (mm-40) REVERT: A 73 LYS cc_start: 0.8684 (mttp) cc_final: 0.8088 (mttt) REVERT: A 78 LYS cc_start: 0.8449 (mmtp) cc_final: 0.7581 (mptt) REVERT: A 82 HIS cc_start: 0.7575 (m170) cc_final: 0.7129 (m170) REVERT: A 208 ARG cc_start: 0.6960 (mtm-85) cc_final: 0.6250 (mmm-85) REVERT: A 222 GLU cc_start: 0.7173 (pm20) cc_final: 0.6744 (pt0) REVERT: A 242 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6715 (tt0) REVERT: B 57 LYS cc_start: 0.8454 (pttm) cc_final: 0.7907 (ptpt) REVERT: B 134 ARG cc_start: 0.6682 (ptm-80) cc_final: 0.5921 (tpp-160) REVERT: B 155 ASN cc_start: 0.6916 (p0) cc_final: 0.6656 (t0) REVERT: B 186 ASP cc_start: 0.8019 (m-30) cc_final: 0.7647 (m-30) REVERT: B 188 MET cc_start: 0.8017 (mmm) cc_final: 0.7568 (mmm) REVERT: B 197 ARG cc_start: 0.7190 (mtm180) cc_final: 0.6851 (mtp85) REVERT: B 212 ASP cc_start: 0.7731 (t0) cc_final: 0.7463 (t70) REVERT: B 214 ARG cc_start: 0.7567 (mmt180) cc_final: 0.7327 (mpp-170) REVERT: B 234 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: B 263 THR cc_start: 0.8352 (t) cc_final: 0.7849 (m) REVERT: B 329 THR cc_start: 0.8670 (m) cc_final: 0.8331 (p) REVERT: G 37 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7068 (mp) REVERT: G 42 GLU cc_start: 0.7085 (pp20) cc_final: 0.6611 (mm-30) outliers start: 28 outliers final: 14 residues processed: 168 average time/residue: 1.3990 time to fit residues: 249.2991 Evaluate side-chains 156 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 297 LYS Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.0670 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN A 75 GLN B 32 GLN B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8467 Z= 0.200 Angle : 0.524 9.805 11489 Z= 0.275 Chirality : 0.043 0.178 1306 Planarity : 0.003 0.029 1450 Dihedral : 4.641 54.332 1280 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.60 % Allowed : 18.58 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.26), residues: 1032 helix: 2.12 (0.27), residues: 391 sheet: 0.51 (0.32), residues: 229 loop : -0.57 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.007 0.001 HIS A 209 PHE 0.012 0.002 PHE B 151 TYR 0.014 0.001 TYR R 129 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.972 Fit side-chains REVERT: R 122 ASP cc_start: 0.7922 (t70) cc_final: 0.7518 (t70) REVERT: R 136 LEU cc_start: 0.7281 (tt) cc_final: 0.6997 (tp) REVERT: R 166 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.6792 (tt0) REVERT: R 200 VAL cc_start: 0.7324 (OUTLIER) cc_final: 0.7058 (p) REVERT: R 298 HIS cc_start: 0.7109 (t70) cc_final: 0.6082 (m-70) REVERT: A 10 LYS cc_start: 0.6874 (mttt) cc_final: 0.6592 (mmtp) REVERT: A 15 ARG cc_start: 0.6339 (ttt90) cc_final: 0.6091 (ttt-90) REVERT: A 20 GLU cc_start: 0.6509 (tp30) cc_final: 0.6119 (tp30) REVERT: A 73 LYS cc_start: 0.8686 (mttp) cc_final: 0.8258 (mttt) REVERT: A 78 LYS cc_start: 0.8471 (mmtp) cc_final: 0.7637 (mptt) REVERT: A 82 HIS cc_start: 0.7565 (m170) cc_final: 0.7241 (m170) REVERT: A 208 ARG cc_start: 0.7018 (mtm-85) cc_final: 0.6274 (mmm-85) REVERT: A 222 GLU cc_start: 0.7214 (pm20) cc_final: 0.6789 (pt0) REVERT: A 242 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6806 (mt-10) REVERT: B 57 LYS cc_start: 0.8465 (pttm) cc_final: 0.8030 (pttt) REVERT: B 59 TYR cc_start: 0.8144 (OUTLIER) cc_final: 0.7490 (t80) REVERT: B 134 ARG cc_start: 0.6737 (ptm-80) cc_final: 0.6017 (tpp-160) REVERT: B 155 ASN cc_start: 0.6991 (p0) cc_final: 0.6687 (t0) REVERT: B 186 ASP cc_start: 0.8040 (m-30) cc_final: 0.7711 (m-30) REVERT: B 188 MET cc_start: 0.8061 (mmm) cc_final: 0.7617 (mmm) REVERT: B 197 ARG cc_start: 0.7099 (mtm180) cc_final: 0.6842 (mtp85) REVERT: B 212 ASP cc_start: 0.7720 (t0) cc_final: 0.7462 (t0) REVERT: B 214 ARG cc_start: 0.7580 (mmt180) cc_final: 0.7261 (mpp-170) REVERT: B 234 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.7555 (m-80) REVERT: B 263 THR cc_start: 0.8358 (t) cc_final: 0.7837 (m) REVERT: B 329 THR cc_start: 0.8685 (m) cc_final: 0.8422 (t) REVERT: G 37 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7135 (mp) REVERT: G 42 GLU cc_start: 0.7116 (pp20) cc_final: 0.6629 (mm-30) outliers start: 32 outliers final: 19 residues processed: 163 average time/residue: 1.4177 time to fit residues: 244.2371 Evaluate side-chains 159 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 297 LYS Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN R 168 GLN A 75 GLN B 32 GLN B 175 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8467 Z= 0.183 Angle : 0.516 13.925 11489 Z= 0.268 Chirality : 0.042 0.196 1306 Planarity : 0.003 0.029 1450 Dihedral : 4.575 50.681 1280 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.04 % Allowed : 19.71 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.26), residues: 1032 helix: 2.21 (0.27), residues: 390 sheet: 0.53 (0.33), residues: 220 loop : -0.57 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS A 209 PHE 0.012 0.001 PHE B 151 TYR 0.014 0.001 TYR R 129 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.995 Fit side-chains REVERT: R 122 ASP cc_start: 0.7907 (t70) cc_final: 0.7494 (t70) REVERT: R 136 LEU cc_start: 0.7277 (tt) cc_final: 0.6989 (tp) REVERT: R 166 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.6801 (tt0) REVERT: R 200 VAL cc_start: 0.7294 (OUTLIER) cc_final: 0.7073 (p) REVERT: R 298 HIS cc_start: 0.7145 (t70) cc_final: 0.6071 (m-70) REVERT: A 10 LYS cc_start: 0.6800 (mttt) cc_final: 0.6476 (mmtm) REVERT: A 15 ARG cc_start: 0.6322 (ttt90) cc_final: 0.6054 (ttt-90) REVERT: A 20 GLU cc_start: 0.6502 (tp30) cc_final: 0.6121 (tp30) REVERT: A 73 LYS cc_start: 0.8631 (mttp) cc_final: 0.8190 (mttt) REVERT: A 78 LYS cc_start: 0.8455 (mmtp) cc_final: 0.7632 (mptt) REVERT: A 82 HIS cc_start: 0.7536 (m170) cc_final: 0.7182 (m170) REVERT: A 208 ARG cc_start: 0.6983 (mtm-85) cc_final: 0.6249 (mmm-85) REVERT: A 222 GLU cc_start: 0.7197 (pm20) cc_final: 0.6761 (pt0) REVERT: A 242 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6736 (mt-10) REVERT: B 57 LYS cc_start: 0.8451 (pttm) cc_final: 0.7995 (pttt) REVERT: B 59 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7367 (t80) REVERT: B 134 ARG cc_start: 0.6651 (ptm-80) cc_final: 0.5897 (tpp-160) REVERT: B 155 ASN cc_start: 0.7002 (p0) cc_final: 0.6707 (t0) REVERT: B 186 ASP cc_start: 0.8032 (m-30) cc_final: 0.7685 (m-30) REVERT: B 212 ASP cc_start: 0.7719 (t0) cc_final: 0.7448 (t0) REVERT: B 214 ARG cc_start: 0.7624 (mmt180) cc_final: 0.7301 (mpp-170) REVERT: B 234 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: B 258 ASP cc_start: 0.6552 (t70) cc_final: 0.6178 (t70) REVERT: B 263 THR cc_start: 0.8330 (t) cc_final: 0.7804 (m) REVERT: B 329 THR cc_start: 0.8674 (m) cc_final: 0.8337 (p) REVERT: G 37 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7111 (mp) REVERT: G 42 GLU cc_start: 0.7095 (pp20) cc_final: 0.6625 (mm-30) outliers start: 27 outliers final: 17 residues processed: 156 average time/residue: 1.4036 time to fit residues: 231.2938 Evaluate side-chains 155 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 297 LYS Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 0.0980 chunk 96 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 67 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8467 Z= 0.145 Angle : 0.493 14.244 11489 Z= 0.255 Chirality : 0.041 0.208 1306 Planarity : 0.003 0.028 1450 Dihedral : 4.388 48.302 1280 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.70 % Allowed : 20.38 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.26), residues: 1032 helix: 2.40 (0.27), residues: 390 sheet: 0.56 (0.33), residues: 219 loop : -0.51 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.011 0.001 PHE B 151 TYR 0.015 0.001 TYR R 129 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: R 122 ASP cc_start: 0.7877 (t70) cc_final: 0.7507 (t70) REVERT: R 136 LEU cc_start: 0.7227 (tt) cc_final: 0.6934 (tp) REVERT: R 166 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6691 (tt0) REVERT: R 200 VAL cc_start: 0.7290 (OUTLIER) cc_final: 0.7084 (p) REVERT: R 268 ARG cc_start: 0.6469 (mtm110) cc_final: 0.6267 (mmm-85) REVERT: R 298 HIS cc_start: 0.7161 (t70) cc_final: 0.6064 (m-70) REVERT: A 10 LYS cc_start: 0.6802 (mttt) cc_final: 0.6513 (mmtp) REVERT: A 15 ARG cc_start: 0.6258 (ttt90) cc_final: 0.5993 (ttt-90) REVERT: A 17 LYS cc_start: 0.6826 (mttt) cc_final: 0.6558 (mttt) REVERT: A 20 GLU cc_start: 0.6526 (tp30) cc_final: 0.6127 (tp30) REVERT: A 73 LYS cc_start: 0.8576 (mttp) cc_final: 0.8063 (mttt) REVERT: A 78 LYS cc_start: 0.8422 (mmtp) cc_final: 0.7605 (mptt) REVERT: A 82 HIS cc_start: 0.7579 (m170) cc_final: 0.7102 (m170) REVERT: A 208 ARG cc_start: 0.6963 (mtm-85) cc_final: 0.6261 (mmm-85) REVERT: A 222 GLU cc_start: 0.7153 (pm20) cc_final: 0.6718 (pt0) REVERT: A 242 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6714 (mt-10) REVERT: B 35 ASN cc_start: 0.7629 (t0) cc_final: 0.7258 (t0) REVERT: B 57 LYS cc_start: 0.8444 (pttm) cc_final: 0.8023 (pttt) REVERT: B 59 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.7066 (t80) REVERT: B 155 ASN cc_start: 0.6961 (p0) cc_final: 0.6681 (t0) REVERT: B 186 ASP cc_start: 0.7719 (m-30) cc_final: 0.7487 (m-30) REVERT: B 197 ARG cc_start: 0.7140 (mtp85) cc_final: 0.6850 (mtp85) REVERT: B 212 ASP cc_start: 0.7658 (t0) cc_final: 0.7345 (t70) REVERT: B 234 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.7545 (m-80) REVERT: B 258 ASP cc_start: 0.6226 (t70) cc_final: 0.5887 (t70) REVERT: B 263 THR cc_start: 0.8323 (t) cc_final: 0.7812 (m) REVERT: B 329 THR cc_start: 0.8655 (m) cc_final: 0.8325 (p) REVERT: G 37 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7022 (mp) REVERT: G 42 GLU cc_start: 0.7068 (pp20) cc_final: 0.6617 (mm-30) outliers start: 24 outliers final: 15 residues processed: 158 average time/residue: 1.3672 time to fit residues: 228.8679 Evaluate side-chains 156 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 297 LYS Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 11 optimal weight: 0.0010 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8467 Z= 0.157 Angle : 0.503 14.601 11489 Z= 0.260 Chirality : 0.041 0.143 1306 Planarity : 0.003 0.028 1450 Dihedral : 4.407 50.598 1280 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.48 % Allowed : 20.50 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.26), residues: 1032 helix: 2.43 (0.27), residues: 390 sheet: 0.52 (0.33), residues: 221 loop : -0.48 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.011 0.001 PHE B 199 TYR 0.009 0.001 TYR N 95 ARG 0.004 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.012 Fit side-chains REVERT: R 122 ASP cc_start: 0.7886 (t70) cc_final: 0.7469 (t70) REVERT: R 136 LEU cc_start: 0.7188 (tt) cc_final: 0.6903 (tp) REVERT: R 166 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6693 (tt0) REVERT: R 196 TYR cc_start: 0.8146 (t80) cc_final: 0.7881 (t80) REVERT: R 200 VAL cc_start: 0.7304 (OUTLIER) cc_final: 0.7068 (p) REVERT: R 268 ARG cc_start: 0.6474 (mtm110) cc_final: 0.6268 (mmm-85) REVERT: R 298 HIS cc_start: 0.7187 (t70) cc_final: 0.6083 (m-70) REVERT: A 10 LYS cc_start: 0.6812 (mttt) cc_final: 0.6492 (mmtm) REVERT: A 15 ARG cc_start: 0.6270 (ttt90) cc_final: 0.5999 (ttt-90) REVERT: A 17 LYS cc_start: 0.6836 (mttt) cc_final: 0.6549 (mttt) REVERT: A 20 GLU cc_start: 0.6524 (tp30) cc_final: 0.6125 (tp30) REVERT: A 73 LYS cc_start: 0.8580 (mttp) cc_final: 0.8055 (mttt) REVERT: A 78 LYS cc_start: 0.8414 (mmtp) cc_final: 0.7594 (mptt) REVERT: A 82 HIS cc_start: 0.7522 (m170) cc_final: 0.7062 (m170) REVERT: A 208 ARG cc_start: 0.6975 (mtm-85) cc_final: 0.6268 (mmm-85) REVERT: A 222 GLU cc_start: 0.7152 (pm20) cc_final: 0.6697 (pt0) REVERT: A 242 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6715 (mt-10) REVERT: B 35 ASN cc_start: 0.7698 (t0) cc_final: 0.7359 (t0) REVERT: B 57 LYS cc_start: 0.8461 (pttm) cc_final: 0.8025 (pttt) REVERT: B 59 TYR cc_start: 0.8127 (OUTLIER) cc_final: 0.7177 (t80) REVERT: B 155 ASN cc_start: 0.6964 (p0) cc_final: 0.6695 (t0) REVERT: B 186 ASP cc_start: 0.7820 (m-30) cc_final: 0.7612 (m-30) REVERT: B 212 ASP cc_start: 0.7657 (t0) cc_final: 0.7273 (t0) REVERT: B 234 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: B 258 ASP cc_start: 0.6261 (t70) cc_final: 0.5922 (t70) REVERT: B 263 THR cc_start: 0.8339 (t) cc_final: 0.7817 (m) REVERT: B 329 THR cc_start: 0.8670 (m) cc_final: 0.8324 (p) REVERT: G 37 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7035 (mp) REVERT: G 42 GLU cc_start: 0.7080 (pp20) cc_final: 0.6625 (mm-30) outliers start: 22 outliers final: 16 residues processed: 153 average time/residue: 1.3823 time to fit residues: 223.5829 Evaluate side-chains 155 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 297 LYS Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN R 168 GLN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.155963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.121440 restraints weight = 8894.665| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.92 r_work: 0.3312 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8467 Z= 0.157 Angle : 0.501 15.042 11489 Z= 0.259 Chirality : 0.041 0.143 1306 Planarity : 0.003 0.028 1450 Dihedral : 4.401 52.208 1280 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.48 % Allowed : 20.38 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.26), residues: 1032 helix: 2.48 (0.26), residues: 390 sheet: 0.51 (0.33), residues: 221 loop : -0.45 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.011 0.001 PHE B 199 TYR 0.009 0.001 TYR N 95 ARG 0.004 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4093.26 seconds wall clock time: 73 minutes 34.53 seconds (4414.53 seconds total)